[gmx-users] on the Umbrella Sampling on-line tutorial

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 3 12:58:59 CEST 2012

Acoot Brett wrote:
> Dear All,
> I planned to use the method introduced in the Umbrella Sampling on-line 
> tutorial of *Justin Lemkul 
> *(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html). 
> But if a peptide is surrounded by a protein, which means the opening of 
> the protein-complex is not large enough to allow the peptide to leave 
> the protein without significantly breaking the conformation of the 
> protein in the protein-peptide complex, is the Umbrella Sampling method 
> still valid for the binding energy calculation?

Chris already gave a very thorough answer to this question.

> Will you please also show me in which part of the tutorial the direction 
> of pull-apart is defined? We should process it in a direction the 
> peptide can leave the protein, not the direction protein will bind the 
> peptide much strongly.

In the tutorial, the dissociation of one peptide from the complex is in step 5. 
  Note that the .mdp files and general procedure that you may need would be 
significantly different from the approach used in the tutorial, if it is at all 
possible to do what you're looking to.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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